Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999998 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:33048539T>AN/A show variant in all transcripts   IGV
HGNC symbol HLA-DPB1
Ensembl transcript ID ENST00000418931
Genbank transcript ID NM_002121
UniProt peptide P04440
alteration type single base exchange
alteration region CDS
DNA changes c.191T>A
cDNA.307T>A
g.4837T>A
AA changes F64Y Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 64
frameshift no
known variant Reference ID: rs1042117
databasehomozygous (A/A)heterozygousallele carriers
1000G189667856
ExAC13801131412694
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1470.064
-1.9440
(flanking)0.0880
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased4829wt: 0.9796 / mu: 0.9884 (marginal change - not scored)wt: AACCGGGAGGAGTTC
mu: AACCGGGAGGAGTAC		 CCGG|gagg
distance from splice site 91
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      64FLERYIYNREEFARFDSDVGEFRA
mutated  all conserved    64REEYARFDSDVGEFR
Ptroglodytes  all conserved  ENSPTRG00000018030  64REEYARFDSDVGEFR
Mmulatta  all conserved  ENSMMUG00000019367  41YLERYIYNREEYVRFDSDVGEFR
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  53YLASYSFNKVVDTQFNSSV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
30121REGIONBeta-1.lost
30225TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 777 / 777
position (AA) of stopcodon in wt / mu AA sequence 259 / 259
position of stopcodon in wt / mu cDNA 893 / 893
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 117 / 117
chromosome 6
strand 1
last intron/exon boundary 898
theoretical NMD boundary in CDS 731
length of CDS 777
coding sequence (CDS) position 191
cDNA position
(for ins/del: last normal base / first normal base)		 307
gDNA position
(for ins/del: last normal base / first normal base)		 4837
chromosomal position
(for ins/del: last normal base / first normal base)		 33048539
original gDNA sequence snippet CATCTACAACCGGGAGGAGTTCGCGCGCTTCGACAGCGACG
altered gDNA sequence snippet CATCTACAACCGGGAGGAGTACGCGCGCTTCGACAGCGACG
original cDNA sequence snippet CATCTACAACCGGGAGGAGTTCGCGCGCTTCGACAGCGACG
altered cDNA sequence snippet CATCTACAACCGGGAGGAGTACGCGCGCTTCGACAGCGACG
wildtype AA sequence MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN
REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRMCRHNY ELGGPMTLQR
RVQPRVNVSP SKKGPLQHHN LLVCHVTDFY PGSIQVRWFL NGQEETAGVV STNLIRNGDW
TFQILVMLEM TPQQGDVYTC QVEHTSLDSP VTVEWKAQSD SARSKTLTGA GGFVLGLIIC
GVGIFMHRRS KKVQRGSA*
mutated AA sequence MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN
REEYARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRMCRHNY ELGGPMTLQR
RVQPRVNVSP SKKGPLQHHN LLVCHVTDFY PGSIQVRWFL NGQEETAGVV STNLIRNGDW
TFQILVMLEM TPQQGDVYTC QVEHTSLDSP VTVEWKAQSD SARSKTLTGA GGFVLGLIIC
GVGIFMHRRS KKVQRGSA*
speed 0.60 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project